6,7-Di­hydro-5H-pyrrolo­[1,2-a]imidazole

In the title compound, the pyrrolidine ring fused to the imidazole ring has an envelope conformation.

Abstract

The crystal structure of 6,7-di­hydro-5H-pyrrolo­[1,2-a]imidazole, C₆H₈N₂, at 100 K has monoclinic (P2₁/n) symmetry. The mol­ecule adopts an envelope conformation of the pyrrolidine ring, which might help for the relief torsion tension. The crystal cohesion is achieved by C—H⋯N hydrogen bonds. Inter­estingly, this fused ring system provides protection of the α-C atom (attached to the non-bridging N atom of the imidazole ring), which provides stability that is of inter­est with respect to electrochemical properties as electrolytes for fuel cells and batteries, and electrodeposition.

Structure description

Ionic liquids have emerged as a promising area in material science because of their tunable properties, allowing them to be used in a wide range of application such as: carbon dioxide capture, fuel cells, nanoparticle stabilization, and many more (Song et al., 2019 ▸; Huang et al., 2017 ▸; Wang et al., 2017 ▸). In this context, our group has been working on the synthesis of new cation moieties for ionic liquid designs. From the different chemical entities employed in ionic liquids, imidazolium derivatives are widely used in the field due to their versatility and relatively high stability. Imidazolium ionic liquid research is dominated by fluorine containing anions (Xue et al., 2006 ▸). Thus, we intended to explore imidazole derivatives (II) at position 2 of the principal structural component, imidazole (I), in order to decrease its reactivity (Fig. 1 ▸).

Figure 1.

Schematic representation of imidazole (I) with atom numbering and of the title derivative (II).

To understand how cations and anions inter­act in ionic liquids, characterization of the starting materials is important. Towards that end, the crystal structure of 6,7-di­hydro-5H-pyrrolo­[1,2-a]imidazole (II) is presented in order to characterize and establish a structure stability relationship of cyclic imidazole derivative families for imidazolium ionic liquid research applications.

The mol­ecular structure of imidazole derivative (II) is displayed in Fig. 2 ▸. We initially envisioned that the electronic and steric effects would be similar to a pyrrole fused to the imidazole moiety and, thus, provide comparison to pyrrolidine below. In order to put into perspective the results found in the mol­ecular and crystal structure of (II), we compare the fused imidazole moiety of (II) with the imidazole crystal structure. There is no significant difference in bond length of the imidazole moiety of (II) compared to the imidazole crystal structure (McMullan et al., 1979 ▸). However, the C2—N2 (N3—C4 in imidazole; McMullan et al., 1979 ▸) bond length of (II) is larger than the same bond found in the imidazole crystal structure [1.390 (2) vs1.375 (1) Å]. This bond-length difference might be due to the new substituted imidazole ring system, which can help justify the chemical shifts observed in the ¹H-NMR spectrum between (II) and (I) of those hydrogen atoms in C1 and C2 of (II), based on the inductive effects of the substituents. On the other hand, we also compare the pyrrolidine fused ring to the pyrrolidine crystal structure (Dziubek & Katrusiak, 2011 ▸). We found that the major bond length difference occurs between bonds N1—C3 and C3—C4 [1.353 (2) vs 1.457 (2) Å and 1.492 (2) vs 1.528 (2) Å], respectively; only the shortest bond length of pyrrolidine was used due to its symmetry). The C5—C6 bond length was found to be 1.543 (2) Å, which is slightly larger than the one found for pyrrolidine [1.528 (2) Å]. These differences in bond length could be attributed to the new sp ² carbon atom (C3) of (II), which also might be responsible for the differences in bond angles in (II). For example, angles N1—C3—C4 and C6—N1—C3 within the fused ring system are much larger compared to those of the pyrrolidine structure [111.1 (1) vs 107.2 (1) and 113.99 (9) vs 103.37 (1) Å, respectively], but angle N1—C6—C5 [102.10 (9) vs 107.05 (1) Å] becomes smaller. These angle differences, despite being small, can help relieve the ring’s stress. Finally, it is important to point out that N1 in pyrrolidine is out of plane (envelope conformation) in order to reduce lone-pair inter­actions, but in (II), this envelope conformation is adopted by C5 as the flap atom where C5 is 0.317 (2) Å out of the plane of the remaining four atoms. Also, the imidazole ring and the planar part of the pyrrolidine ring make a dihedral angle of 3.85 (9)°. By N1 becoming part of the plane, its lone pairs could add new repulsion inter­actions, suggesting why the ring has to adapt to this conformation to avoid repulsions.

Figure 2.

The mol­ecular structure of (II) showing the atom-labeling scheme. Displacement ellipsoids are scaled to the 50% probability level.

A look into possible inter­molecular hydrogen-bonding inter­actions of (II), we found a value of 3.37 (3) Å between C1⋯N2, indicative of a weak hydrogen bond (Fig. 3 ▸, Table 1 ▸) that leads to the formation of supra­molecular chains extending parallel to [101]. Nevertheless, we believe that the major inter­molecular force contribution to the stabilization of the crystal structure is by aliphatic C—H⋯π inter­actions. We observed how C6 (non-aromatic ring atom) inter­acts with C2ⁱ, N2ⁱ, and C3ⁱ [distances are 3.672 (3), 3.692 (4), and 3.620 (3), respectively; symmetry code: (i) −x + 1, −y + 2, −z). Analyzing the possibility of any π–π inter­actions we determine that due to the reciprocal stacking of the mol­ecules and the offset distance of the aromatic centroids (4.487 Å), we suggest that the possibility of a π–π inter­action between the mol­ecules is not found. We conclude that C—H⋯π inter­actions, although weak compared to a conventional hydrogen bond, could serve together with other inter­molecular forces to impose directionality and order through the crystal lattice. Previously, C—H⋯π inter­actions have been proven to show stability in crystal structures. In fact, it has been suggested that aliphatic–aromatic inter­actions could play a greater stabilization role than aromatic–aromatic inter­actions (Ninković et al., 2016 ▸; Carmona-Negrón et al., 2016 ▸). Fig. 3 ▸ shows the packing diagram of (II).

Figure 3.

Packing diagram for (II) projected along the b axis (A), and the inter­molecular arrangement and distance of (II) found in the crystal structure (B) (a shows the centroid-to-centroid distance, b the centroid-to-atom distance). Hydrogen atoms were omitted for clarity.

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C1—H1⋯N2	0.95 (1)	2.52 (1)	3.73 (3)	150 (1)

Synthesis and crystallization

The compound was synthesized following a literature procedure with a modification (Kan et al., 2007 ▸). Hydrogen chloride was bubbled into a solution of 4-chloro­butyro­nitrile (10 g, 274 mmol) and methanol (11.65 ml, 288 mmol) in ether (135 ml). The solution was treated with hydrogen chloride at room temperature until saturated. After 24 h of reaction, the white precipitate was washed with ether and dried under vacuum to afford the imidate. ¹H NMR (400 MHz, CDCl₃) δ 12.51 (s, 1H), 11.60 (s, 1H), 4.26 (s, 3H), 3.57 (t, J = 6.1 Hz, 2H), 2.92 (t, J = 6.6 Hz, 2H), 2.19 (q, J = 6.3 Hz, 2H).

To a solution of the imidate (34 g, 198 mmol) in di­chloro­methane (200 ml), amino­acetaldehyde (20.78 g, 198 mmol) and tri­ethyl­amine (60 g, 593 mmol) were added and heated to 333 K for 2 h to afford the amidine inter­mediary, which was dried under vacuum. The amidine was stirred in formic acid at 353 K for 20 h. Solid sodium bicarbonate was added to the solution to raise the pH to 10. The solution was extracted with di­chloro­methane (3 × 100 ml) and dried over anhydrous Na₂SO₄. Filtration and evaporation under reduced pressure was followed by sublimation to afford a crystalline solid (12.7 g, 60% yield in two steps); m.p. 338 K; ¹H NMR (400 MHz, DMSO-d ₆) δ 7.02 (d, J = 1.3 Hz, 1H), 6.85 (d, J = 1.3 Hz, 1H), 3.89 (dd, J = 7.6, 6.6 Hz, 2H), 2.66 (m, 2H), 2.44 (m, 2H).

Crystals of the title compound grew as very large, colorless prisms by slow sublimation at 313 K and 1.5 mbar. The crystal under investigation was cut from a larger crystal.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2 ▸.

Table 2. Experimental details.

Crystal data
Chemical formula	C6H8N2
M r	108.14
Crystal system, space group	Monoclinic, P21/n
Temperature (K)	100
a, b, c (Å)	7.908 (7), 7.441 (8), 9.880 (9)
β (°)	104.91 (3)
V (Å3)	561.8 (9)
Z	4
Radiation type	Mo Kα
μ (mm−1)	0.08
Crystal size (mm)	0.31 × 0.19 × 0.16
Data collection
Diffractometer	Rigaku AFC-12 with Saturn 724+ CCD
Absorption correction	Multi-scan (ABSCOR; Higashi, 2001 ▸)
T min, T max	0.730, 1.00
No. of measured, independent and observed [I > 2σ(I)] reflections	2575, 1279, 1028
R int	0.036
(sin θ/λ)max (Å−1)	0.649
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S	0.042, 0.123, 1.05
No. of reflections	1279
No. of parameters	105
H-atom treatment	All H-atom parameters refined
Δρmax, Δρmin (e Å−3)	0.28, −0.22

Computer programs: CrystalClear (Rigaku, 2008 ▸), SHELXT (Sheldrick, 2015a ▸), SHELXL (Sheldrick, 2015b ▸), XP in SHELXTL/PC (Sheldrick, 2008 ▸), Mercury Macrae et al., 2020 ▸) and publCIF (Westrip, 2010 ▸).

Supplementary Material

CCDC reference: 1912032

Additional supporting information: crystallographic information; 3D view; checkCIF report

full crystallographic data

Crystal data

C6H8N2	F(000) = 232
Mr = 108.14	Dx = 1.279 Mg m−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
a = 7.908 (7) Å	Cell parameters from 1451 reflections
b = 7.441 (8) Å	θ = 2.7–27.5°
c = 9.880 (9) Å	µ = 0.08 mm−1
β = 104.91 (3)°	T = 100 K
V = 561.8 (9) Å3	Prism, colorless
Z = 4	0.31 × 0.19 × 0.16 mm

Data collection

Rigaku AFC-12 with Saturn 724+ CCD diffractometer	1028 reflections with I > 2σ(I)
Radiation source: sealed fine focus tube	Rint = 0.036
ω–scans	θmax = 27.5°, θmin = 3.0°
Absorption correction: multi-scan (ABSCOR; Higashi, 2001)	h = −6→10
Tmin = 0.730, Tmax = 1.00	k = −6→9
2575 measured reflections	l = −12→12
1279 independent reflections

Refinement

Refinement on F2	0 restraints
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.042	All H-atom parameters refined
wR(F2) = 0.123	w = 1/[σ2(Fo2) + (0.0797P)2] where P = (Fo2 + 2Fc2)/3
S = 1.05	(Δ/σ)max < 0.001
1279 reflections	Δρmax = 0.28 e Å−3
105 parameters	Δρmin = −0.22 e Å−3

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C1	0.35368 (15)	0.73358 (16)	0.04868 (12)	0.0174 (3)
C2	0.25317 (16)	0.68855 (17)	−0.08171 (12)	0.0197 (3)
C3	0.20769 (14)	0.96844 (16)	−0.05783 (11)	0.0156 (3)
C4	0.17443 (17)	1.16552 (17)	−0.05457 (13)	0.0209 (3)
C5	0.26013 (17)	1.21318 (18)	0.10150 (13)	0.0219 (3)
C6	0.38632 (16)	1.05792 (16)	0.16201 (12)	0.0183 (3)
N1	0.32126 (12)	0.91323 (13)	0.06209 (9)	0.0150 (3)
N2	0.16179 (13)	0.83657 (14)	−0.14934 (10)	0.0194 (3)
H1	0.4341 (18)	0.6695 (18)	0.1200 (15)	0.024 (4)*
H2	0.2433 (17)	0.5700 (17)	−0.1276 (14)	0.023 (4)*
H4A	0.2310 (17)	1.2310 (17)	−0.1188 (14)	0.023 (4)*
H4B	0.0496 (19)	1.1952 (19)	−0.0828 (15)	0.029 (4)*
H5A	0.3296 (19)	1.333 (2)	0.1160 (16)	0.032 (4)*
H5B	0.167 (2)	1.2194 (19)	0.1527 (15)	0.035 (4)*
H6A	0.5118 (17)	1.0873 (18)	0.1648 (13)	0.022 (3)*
H6B	0.3805 (18)	1.018 (2)	0.2585 (15)	0.036 (4)*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
C1	0.0210 (6)	0.0136 (6)	0.0166 (6)	−0.0006 (5)	0.0029 (5)	0.0022 (5)
C2	0.0246 (6)	0.0159 (7)	0.0177 (6)	−0.0034 (5)	0.0037 (5)	−0.0014 (5)
C3	0.0149 (5)	0.0193 (6)	0.0123 (6)	0.0003 (4)	0.0029 (4)	0.0023 (4)
C4	0.0232 (7)	0.0201 (7)	0.0199 (6)	0.0025 (5)	0.0067 (5)	0.0036 (5)
C5	0.0255 (7)	0.0192 (7)	0.0224 (6)	0.0004 (5)	0.0087 (5)	−0.0032 (5)
C6	0.0238 (6)	0.0178 (6)	0.0128 (6)	−0.0054 (5)	0.0038 (4)	−0.0037 (4)
N1	0.0174 (5)	0.0158 (6)	0.0111 (5)	−0.0014 (4)	0.0021 (4)	−0.0001 (4)
N2	0.0207 (5)	0.0210 (6)	0.0155 (5)	−0.0017 (4)	0.0025 (4)	−0.0004 (4)

Geometric parameters (Å, º)

C1—C2	1.3700 (19)	C4—H4A	0.993 (14)
C1—N1	1.374 (2)	C4—H4B	0.980 (15)
C1—H1	0.948 (14)	C5—C6	1.543 (2)
C2—N2	1.3905 (18)	C5—H5A	1.038 (15)
C2—H2	0.986 (13)	C5—H5B	0.994 (15)
C3—N2	1.3203 (18)	C6—N1	1.4619 (17)
C3—N1	1.3533 (17)	C6—H6A	1.010 (13)
C3—C4	1.492 (2)	C6—H6B	1.011 (14)
C4—C5	1.557 (2)
C2—C1—N1	104.54 (10)	C6—C5—H5A	108.9 (8)
C2—C1—H1	133.8 (8)	C4—C5—H5A	114.4 (8)
N1—C1—H1	121.6 (8)	C6—C5—H5B	109.0 (8)
C1—C2—N2	111.23 (12)	C4—C5—H5B	108.9 (8)
C1—C2—H2	127.5 (8)	H5A—C5—H5B	108.9 (12)
N2—C2—H2	121.2 (8)	N1—C6—C5	102.10 (11)
N2—C3—N1	112.18 (12)	N1—C6—H6A	110.5 (7)
N2—C3—C4	136.59 (11)	C5—C6—H6A	112.4 (8)
N1—C3—C4	111.13 (10)	N1—C6—H6B	109.0 (9)
C3—C4—C5	102.18 (10)	C5—C6—H6B	113.8 (9)
C3—C4—H4A	111.0 (8)	H6A—C6—H6B	108.7 (10)
C5—C4—H4A	111.6 (8)	C3—N1—C1	108.01 (10)
C3—C4—H4B	112.7 (8)	C3—N1—C6	113.99 (11)
C5—C4—H4B	112.4 (8)	C1—N1—C6	137.70 (10)
H4A—C4—H4B	107.1 (11)	C3—N2—C2	104.03 (12)
C6—C5—C4	106.64 (11)
N1—C3—C4—C5	−10.83 (13)	C4—C3—N1—C6	−1.63 (13)
C3—C4—C5—C6	18.49 (13)	C5—C6—N1—C3	13.39 (12)
C4—C5—C6—N1	−19.28 (13)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1···N2	0.95 (1)	2.52 (1)	3.73 (3)	150 (1)

Selective Supramolecular interaction of II

D···A	Distance
C6-N2	3.692 (4)
C6-C2	3.672 (3)
C6-C3	3.620 (3)

Funding Statement

The data were collected using instrumentation purchased with funds provided by the National Science Foundation grant No. 0741973.